QuickBooks® Online Payroll Tax Filing to Be Automated on July 1
If your organization uses QuickBooks® Online Payroll, there is an important change coming on July 1, 2026, that requires your attention and action before the deadline.
What’s Changing?
Currently, QuickBooks® Online Payroll gives users a choice: you can either have QuickBooks® automatically pay and file your payroll taxes on your behalf or you can handle the payments and filings manually yourself. That flexibility will be ending in the coming months.
Starting July 1, 2026, QuickBooks® Online Payroll will automatically pay and file all payroll taxes that were already set up on your account. The option to manually submit tax payments or file returns through the Payroll Tax Center will be removed, as will the ability to turn off automated taxes as a payroll setting altogether.
Intuit® has stated that this change is designed to save businesses time by eliminating the need to manually track, pay and file payroll taxes.
What Does This Mean for Your Organization?
For clients who were already using the automated tax filing feature, this change will largely be seamless. However, for clients who have been managing their own payroll tax payments and filings manually, this is a significant shift in how your payroll process will work going forward.
Beginning July 1, QuickBooks® will automatically withdraw tax funds directly from your bank account each time you run payroll or whenever your tax liabilities increase. Additionally, if you have any unpaid federal taxes from the current quarter at the time your tax setup is completed, those amounts will be withdrawn immediately upon setup completion.
This makes it critically important that your tax setup within QuickBooks® is accurate and complete and that any payments you have already made outside of QuickBooks® are properly recorded in the system.
What Do You Need to Do?
There are two key action items to address before July 1, 2026:
Complete Your Tax Setup
To avoid any disruption to your payroll runs, the primary admin user should complete all required tax setup steps in QuickBooks® on or before June 30, 2026. Clients who have not finished their tax setup by July 1 may be unable to run payroll until the setup is complete. To check your status and finish any outstanding items, navigate to Payroll Overview in QuickBooks® and review your “To Do” list.
Record Any Payments Already Made Outside QuickBooks®
If you have already made payroll tax payments for the current quarter through channels outside of QuickBooks®, such as directly through the IRS Electronic Federal Tax Payment System (EFTPS) or a state tax portal, it’s essential that you record those payments within QuickBooks® before July 1. To do this, go to the Payroll Tax Center, locate the applicable payments and select “Mark as Paid.” This step ensures QuickBooks® does not attempt to withdraw funds for taxes that have already been remitted, which could result in duplicate payments.
How Can Brown Plus Help?
We understand that changes like this can raise questions, especially when they directly affect your payroll process and bank account activity. Our Outsourced Accounting Services team is experienced in using QuickBooks® Online Payroll and is available to help you navigate this transition, confirm your tax setup is complete and ensure any prior payments are properly recorded in the system.
If you have questions or would like assistance reviewing your QuickBooks® payroll settings ahead of the July 1 deadline, please reach out to your Brown Plus contact or connect with our Outsourced Accounting Services team today.